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David, we're going to try and target a fix for this by 2.7.1.
This fix did not make it into 2.7.1. It will be addressed in a later release.
Fixed the indentation issue and also restored the panel background and border for code blocks.
Can you please provide a 2.6.2 patch for this ? In our organization, code indentation is heavily used by many (there are 2500 wiki users), and after the 2.6.2 upgrade, everybody found that the pdf formatting which used to work in 2.4.3 does not work in 2.6.2.So this was escalated and it was a chaos. It is a matter of concern, and I think you should provide patches for the same.Engineering team,please help.
The attached xhtml2fo.xsl file fixes the missing code macro border and the indentation issue for Confluence 2.6.2.
To install this file you will need to replace the one within your current confluence-2.6.2.jar - remember to back up your original confluence-2.6.2.jar just in case. e.g. in Unix speak
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We have a fairly integrated documentation structure that uses confluence as the source for all our documentation, we then export to PDF and HTML for an secure web site to make available to clients. Over half of our documentation is on APIs: e.g. COM and XML and these make extensive use of the code macro. This export worked fine in v2.2; It is now broken in v2.6 and we need to find a fix before we can export of our API manuals.
Not good!
Note that we had to stick to the code macro and not use the new code macro has issues of it's own:

http://developer.atlassian.com/jira/browse/NCODE-3
http://developer.atlassian.com/jira/browse/NCODE-2